Buggy code:
public class CatalogStudyConfigurationManager extends StudyConfigurationManager { public static final String CATALOG_PROPERTIES_FILE = "catalogPropertiesFile" ; public static final QueryOptions ALL_FILES_QUERY_OPTIONS = new QueryOptions ( ) . append ( bioformat . toString ( ) , Arrays . asList ( VARIANT , ALIGNMENT ) ) . append ( "include" , Arrays . asList ( "projects.studies.files.id" , "projects.studies.files.name" , "projects.studies.files.sampleIds" ) ) ; public static final QueryOptions INDEXED_FILES_QUERY_OPTIONS = new QueryOptions ( ) . append ( ( ( index . toString ( ) ) + ".status" ) , READY ) . append ( "include" , Arrays . asList ( "projects.studies.files.id" , "projects.studies.files.name" ) ) ; public static final QueryOptions SAMPLES_QUERY_OPTIONS = new QueryOptions ( "include" , Arrays . asList ( "projects.studies.samples.id" , "projects.studies.samples.name" ) ) ; public static final QueryOptions COHORTS_QUERY_OPTIONS = new QueryOptions ( ) ; protected static Logger logger = LoggerFactory . getLogger ( CatalogStudyConfigurationManager . class ) ; private final CatalogManager catalogManager ; private final String sessionId ; public static final String STUDY_CONFIGURATION_FIELD = "studyConfiguration" ; public static final QueryOptions STUDY_QUERY_OPTIONS = new QueryOptions ( "include" , Arrays . asList ( "projects.studies.alias" , ( "projects.studies.attributes." + ( CatalogStudyConfigurationManager . STUDY_CONFIGURATION_FIELD ) ) ) ) ; private final ObjectMapper objectMapper ; public CatalogStudyConfigurationManager ( ObjectMap objectMap ) throws CatalogException { } public CatalogStudyConfigurationManager ( CatalogManager catalogManager , String sessionId ) { } @ Override protected QueryResult < StudyConfiguration > _getStudyConfiguration ( String studyName , Long timeStamp , QueryOptions options ) { } @ Override protected QueryResult < StudyConfiguration > _getStudyConfiguration ( int studyId , Long timeStamp , QueryOptions options ) { } private QueryResult < StudyConfiguration > _getStudyConfiguration ( Integer studyId , String studyName , Long timeStamp , QueryOptions options ) { String sessionId = ( options == null ) ? this . sessionId : options . getString ( "sessionId" , this . sessionId ) ; StudyConfiguration studyConfiguration = null ; long start = System . currentTimeMillis ( ) ; try { if ( studyId == null ) { studyId = catalogManager . getStudyId ( studyName ) ; } CatalogStudyConfigurationManager . logger . debug ( "Reading<seq2seq4repair_space>StudyConfiguration<seq2seq4repair_space>from<seq2seq4repair_space>Catalog.<seq2seq4repair_space>studyId:<seq2seq4repair_space>{}" , studyId ) ; <START_BUG> System . out . println ( ( ( "CatalogStudyConfigurationManager<seq2seq4repair_space>-<seq2seq4repair_space>options<seq2seq4repair_space>=<seq2seq4repair_space>" + options ) == null ? null : options . toJson ( ) ) ) ; <END_BUG> Study study = catalogManager . getStudy ( studyId , sessionId , CatalogStudyConfigurationManager . STUDY_QUERY_OPTIONS ) . first ( ) ; studyConfiguration = new StudyConfiguration ( studyId , study . getAlias ( ) ) ; Object o = study . getAttributes ( ) . get ( CatalogStudyConfigurationManager . STUDY_CONFIGURATION_FIELD ) ; if ( ( o != null ) && ( o instanceof Map ) ) { if ( ( ( Long ) ( ( ( Map ) ( o ) ) . get ( "timeStamp" ) ) ) . equals ( timeStamp ) ) { return new QueryResult ( studyName , ( ( int ) ( ( System . currentTimeMillis ( ) ) - start ) ) , 0 , 0 , "" , "" , Collections . emptyList ( ) ) ; } Object attributes = ( ( Map ) ( o ) ) . get ( "attributes" ) ; if ( ( attributes != null ) && ( attributes instanceof Map ) ) { studyConfiguration . getAttributes ( ) . putAll ( ( ( Map ) ( attributes ) ) ) ; } } CatalogStudyConfigurationManager . logger . trace ( "Read<seq2seq4repair_space>StudyConfiguration<seq2seq4repair_space>studyConfiguration<seq2seq4repair_space>{}" , studyConfiguration ) ; QueryResult < File > indexedFiles = catalogManager . getAllFiles ( studyId , CatalogStudyConfigurationManager . INDEXED_FILES_QUERY_OPTIONS , sessionId ) ; for ( File file : indexedFiles . getResult ( ) ) { studyConfiguration . getIndexedFiles ( ) . add ( file . getId ( ) ) ; } QueryResult < File > files = catalogManager . getAllFiles ( studyId , CatalogStudyConfigurationManager . ALL_FILES_QUERY_OPTIONS , sessionId ) ; for ( File file : files . getResult ( ) ) { studyConfiguration . getFileIds ( ) . put ( file . getName ( ) , file . getId ( ) ) ; studyConfiguration . getSamplesInFiles ( ) . put ( file . getId ( ) , new java . util . HashSet ( file . getSampleIds ( ) ) ) ; } QueryResult < Sample > samples = catalogManager . getAllSamples ( studyId , CatalogStudyConfigurationManager . SAMPLES_QUERY_OPTIONS , sessionId ) ; for ( Sample sample : samples . getResult ( ) ) { studyConfiguration . getSampleIds ( ) . put ( sample . getName ( ) , sample . getId ( ) ) ; } QueryResult < Cohort > cohorts = catalogManager . getAllCohorts ( studyId , CatalogStudyConfigurationManager . COHORTS_QUERY_OPTIONS , sessionId ) ; for ( Cohort cohort : cohorts . getResult ( ) ) { studyConfiguration . getCohortIds ( ) . put ( cohort . getName ( ) , cohort . getId ( ) ) ; studyConfiguration . getCohorts ( ) . put ( cohort . getId ( ) , new java . util . HashSet ( cohort . getSamples ( ) ) ) ; if ( ( cohort . getStatus ( ) ) == ( Status . READY ) ) { studyConfiguration . getCalculatedStats ( ) . add ( cohort . getId ( ) ) ; } else if ( ( cohort . getStatus ( ) ) == ( Status . INVALID ) ) { studyConfiguration . getInvalidStats ( ) . add ( cohort . getId ( ) ) ; } } } catch ( CatalogException e ) { e . printStackTrace ( ) ; CatalogStudyConfigurationManager . logger . error ( "Unable<seq2seq4repair_space>to<seq2seq4repair_space>get<seq2seq4repair_space>StudyConfiguration<seq2seq4repair_space>from<seq2seq4repair_space>Catalog" , e ) ; } if ( studyConfiguration == null ) { return new QueryResult ( studyName , ( ( int ) ( ( System . currentTimeMillis ( ) ) - start ) ) , 0 , 0 , "" , "" , Collections . emptyList ( ) ) ; }

Fix:
CatalogStudyConfigurationManager . logger . debug ( ( "CatalogStudyConfigurationManager<seq2seq4repair_space>-<seq2seq4repair_space>options<seq2seq4repair_space>=<seq2seq4repair_space>" + ( options == null ? null : options . toJson ( ) ) ) ) ;